First sequence in alignment is "special" ?

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file

http://sanger-pathogens.github.io/snp-sites/

Other

233 stars 50 forks source link

First sequence in alignment is "special" ? #25

Closed tseemann closed 8 years ago

tseemann commented 8 years ago

I was wondering if the first sequence in the alignment is considered "special" in some (undocumented) way?

I see the code does something unusual:

       // First sequence is the reference sequence so skip it
       // If there is an indel in the reference sequence, replace with the first proper base you find